Application of computer simulation in optimization of nucleic acid aptamer screening and analysis
WANG Ming-Hua1, LI Du-Juan2
1. Biology Department, Xinzhou Teachers University, Xinzhou 034000, China; 2. College of Life Information Science and Instrument Engineering, Hangzhou Dianzi University, Hangzhou 310018, China
Abstract: This paper reviews and analyzes the applicability,procedure and necessity of the method for virtual screening nucleic acid aptamer assisted by computer simulation,based on listing the successful application examples in screening and studying new trends.It aims to provide a new idea for computer virtual screening technology to promote the development and application of nucleic acid aptamers.
王明华, 李杜娟. 计算机模拟在优化核酸适体筛选分析流程中的应用研究[J]. 现代化工, 2018, 38(11): 216-220.
WANG Ming-Hua, LI Du-Juan. Application of computer simulation in optimization of nucleic acid aptamer screening and analysis. Modern Chemical Industry, 2018, 38(11): 216-220.
[1] Bock L C,Griffin L C,Latham J A,et al.Selection of single-stranded DNA molecules that bind and inhibit human thrombin[J].Nature,1992,355(6360):564-566. [2] Draper D E.Themes in RNA-protein recognition[J].Journal of Molecular Biology,1999,293(2):255-270. [3] Brooks B R,Ma Jr,Nilsson L,et al.CHARMM:The biomolecular simulation program[J].Journal of Computational Chemistry,2009,30(10):1545-1614. [4] Szczesniak M W,Makalowska I.lncRNA-RNA interactions across the human transcriptome[J].PloS One,2016,11:e0150353. [5] Fiannaca A,Rosa M L,Paglia L L,et al.nRC:Non-coding RNA classifier based on structural features[J].Biodata Mining,2017,10(8):e27. [6] Collie G W,Parkinson G N.The application of DNA and RNA G-quadruplexes to therapeutic medicines[J].Chemical Society Reviews,2012,40(12):5867-5892. [7] Nawrocki E P,Burge S W,Bateman A,et al.Rfam 12.0:Updates to the RNA families database[J].Nucleic Acids Research,2015,43(D1):D130-D137. [8] Zuker M.Mfold web server for nucleic acid folding and hybridization prediction[J].Nucleic Acids Research,2003,31(13):3406-3415. [9] Reuter J S,Mathews D H.RNA structure:Software for RNA secondary structure prediction and analysis[J].BMC Bioinformatics,2010,11(1):e129. [10] Miladi M,Junge A,Costa F,et al.RNAscClust:Clustering RNA sequences using structure conservation and graph based motifs[J].Bioinformatics,2017,33(14):2089-2096. [11] Shi J,Li X,Dong M,et al.JNSViewer-A java script-based nucleotide sequence viewer for DNA/RNA secondary structures[J].Plos One,2017,12(6):e0179040. [12] Biesiada M,Purzycka K J,Szachniuk M,et al.Automated RNA 3D structure prediction with RNA composer[J].Methods in Molecular Biology,2016,1490(6):199-215. [13] Das R,Baker D.Automated de novo prediction of native-like RNA tertiary structures[J].Proceedings of the National Academy of Sciences of the United States of America,2007,104:14664-14669. [14] Dijk M V,Bonvin A M J J.3D-DART:A DNA structure modelling server[J].Nucleic Acids Research,2009,37(7):W235-W239. [15] Snodin B E,Romano F,Rovigatti L,et al.Direct simulation of the self-assembly of a small DNA origami[J].Acs Nano,2016,10(2):1724-1737. [16] Jeddi I,Saiz L.Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors[J].Scientific Reports,2017,7(4):e1178. [17] Alexandra S P,Ruth N,Wolfson H J.RsiteDB:A database of protein binding pockets that interact with RNA nucleotide bases[J].Nucleic Acids Research,2009,37(1):D369-D373. [18] Tuyshinjargal N,Lee W,Park B,et al.PRIdictor:Protein-RNA interaction predictor[J].Biosystems,2016,139(1):17-22. [19] Pierce B G,Wiehe K,Hwang H,et al.ZDOCK Server:Interactive docking prediction of protein-protein complexes and symmetric multimers[J].Bioinformatics,2014,30(12):1771-1773. [20] Gray J J,Moughon S,Wang C,et al.Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations[J].Journal of Molecular Biology,2003,331(1):281-299. [21] Tuszynska I,Magnus M,Jonak K,et al.NPDock:A web server for protein-nucleic acid docking[J].Nucleic Acids Research,2015,43(W1):W425-W430. [22] Shcherbinin D S,Gnedenko O V,Khmeleva S A,et al.Computer-aided design of aptamers for cytochrome p450[J].Journal of Structural Biology,2015,191(2):112-119. [23] Heiat M,Najafi A,Ranjbar R,et al.Computational approach to analyze isolated ssDNA aptamers against angiotensin Ⅱ[J].Journal of Biotechnology,2016,230:34-39. [24] Chushak Y,Stone M O.In silico selection of RNA aptamers[J].Nucleic Acids Research,2009,37(12):e87. [25] Savory N,Lednor D,Tsukakoshi K,et al.In silico maturation of binding-specificity of DNA aptamers against proteus mirabilis[J].Biotechnology and Bioengineering,2013,110(10):2573-2580. [26] Savory N,Nzakizwanayo J,Abe K,et al.Selection of DNA aptamers against uropathogenic Escherichia coli NSM59 by quantitative PCR controlled Cell-SELEX[J].Journal of Microbiological Methods,2014,104(9):94-100. [27] Yokoyama T,Tsukakoshi K,Yoshida W,et al.Development of HGF-binding aptamers with the combination of G4 promoter-derived aptamer selection and in silico maturation[J].Biotechnology and Bioengineering,2017,114(10):2196-2203. [28] Fukaya T,Abe K,Savory N,et al.Improvement of the VEGF binding ability of DNA aptamers through in silico maturation and multimerization strategy[J].Journal of Biotechnology,2015,212(6863):99-105. [29] Zhou Q,Xia X,Luo Z.Searching the sequence space for potent aptamers using SELEX in silico[J].Journal of Chemical Theory and Computation,2015,11(12):5939-5946. [30] Ahirwar R,Nahar S,Aggarwal S,et al.In silico selection of an aptamer to estrogen receptor alpha using computational docking employing[J].Scientific reports,2016,6(2):e21285.